Chapter 10 Spirochaetota

Code_bundle Code_element Code_function Domain Function Element Definition
B010301 B0103 B01 Biosynthesis Nucleic acid biosynthesis UDP/UTP (K13800,K13809,K09903)
B010401 B0104 B01 Biosynthesis Nucleic acid biosynthesis CDP/CTP (K00940,K18533) K01937
B010501 B0105 B01 Biosynthesis Nucleic acid biosynthesis ADP/ATP K01939 K01756 (K00939,K18532,K18533,K00944) K00940
B021201 B0212 B02 Biosynthesis Amino acid biosynthesis Arginine K00611 K01940 (K01755,K14681)
B021202 B0212 B02 Biosynthesis Amino acid biosynthesis Arginine K22478 K00145 K00821 K09065 K01438 K01940 K01755
B021301 B0213 B02 Biosynthesis Amino acid biosynthesis Proline ((K00931 K00147),K12657) K00286
B060201 B0602 B06 Biosynthesis Organic anion biosynthesis Fumarate (K01647,K05942) (K01681,K01682) (K00031,K00030) ((((K00164+K00658),K01616)+K00382),(K00174+K00175)) ((K01902+K01903),(K01899+K01900),K18118) ((K00234+K00235+K00236+(K00237,K25801)),(K00239+K00240+K00241),(K00244+K00245+K00246)) (K01676,K01679,(K01677+K01678)) (K00026,K00025,K00024,K00116)
B060202 B0602 B06 Biosynthesis Organic anion biosynthesis Fumarate ((((K00164+K00658),K01616)+K00382),K00174) ((K01902+K01903),(K01899+K01900),K18118) ((K00234+K00235+K00236+(K00237,K25801)),(K00239+K00240+K00241),(K00244+K00245+K00246)) (K01676,K01679,(K01677+K01678)) (K00026,K00025,K00024,K00116)
B060203 B0602 B06 Biosynthesis Organic anion biosynthesis Fumarate K01948 K00611 K01940 (K01755,K14681) K01476
B060204 B0602 B06 Biosynthesis Organic anion biosynthesis Fumarate (K00815,K00838,K00832,K03334) K00457 K00451 K01800 (K01555,K16171)
B060205 B0602 B06 Biosynthesis Organic anion biosynthesis Fumarate K00241+(K00242,K18859,K18860)+K00239+K00240
B060206 B0602 B06 Biosynthesis Organic anion biosynthesis Fumarate K00244+K00245+K00246+K00247
B060207 B0602 B06 Biosynthesis Organic anion biosynthesis Fumarate (K00169+K00170+K00171+K00172) K01007 K01595 K00024 (K01677+K01678) (K00239+K00240) (K01902+K01903) (K15038,K15017) K14465 (K14467,K18861) K14534 K15016 K00626
B060208 B0602 B06 Biosynthesis Organic anion biosynthesis Fumarate (K02160+K01961+K01962+K01963) K14468 K14469 K15052 K05606 (K01847,(K01848+K01849)) (K14471+K14472) (K00239+K00240+K00241) K01679 K08691 K14449 K14470 K09709
B060209 B0602 B06 Biosynthesis Organic anion biosynthesis Fumarate (K00169+K00170+K00171+K00172) (K01959+K01960) K00024 (K01677+K01678) (K18209+K18210) (K01902+K01903) (K00174+K00175+K00176+K00177)
B060210 B0602 B06 Biosynthesis Organic anion biosynthesis Fumarate (K18029+K18030) K14974 K18028 K15357 K13995 K01799
B060211 B0602 B06 Biosynthesis Organic anion biosynthesis Fumarate K00611 K01940 (K01755,K14681)
B060212 B0602 B06 Biosynthesis Organic anion biosynthesis Fumarate K22478 K00145 K00821 K09065 K01438 K01940 K01755
B060213 B0602 B06 Biosynthesis Organic anion biosynthesis Fumarate 2.6.1.1,2.6.1.5,2.6.1.27,2.6.1.57 1.13.11.27 1.13.11.5 5.2.1.2 3.7.1.2
D050101 D0501 D05 Degradation Amino acid degradation Serine 4.3.1.17,4.3.1.18
D060401 D0604 D06 Degradation Nitrogen compound degradation GlcNAc 2.7.1.59 3.5.1.25 3.5.99.6
D060402 D0604 D06 Degradation Nitrogen compound degradation GlcNAc 3.5.1.25 3.5.99.6
D090701 D0907 D09 Degradation Antibiotic degradation Tetracycline K08151,K08168,K18214,K18218,K18220,K18221
             genome D0308      domain               phylum            class                 order
1   EHA03298_bin.15  1.00 d__Bacteria       p__Bacillota_A    c__Clostridia    o__Oscillospirales
2   EHA03305_bin.41  1.00 d__Bacteria      p__Bacteroidota   c__Bacteroidia      o__Bacteroidales
3   EHA03306_bin.10  1.00 d__Bacteria      p__Bacteroidota   c__Bacteroidia      o__Bacteroidales
4    EHA04584_bin.1  1.00 d__Bacteria      p__Bacteroidota   c__Bacteroidia      o__Bacteroidales
5   EHA04588_bin.67  1.00 d__Bacteria       p__Bacillota_A    c__Clostridia o__Christensenellales
6    EHA03303_bin.3  1.00 d__Bacteria       p__Bacillota_A    c__Clostridia     o__Lachnospirales
7   EHA03303_bin.13  1.00 d__Bacteria       p__Bacillota_A    c__Clostridia o__Christensenellales
8  EHA03305_bin.265  1.00 d__Bacteria         p__Bacillota       c__Bacilli   o__Staphylococcales
9   EHA03347_bin.69  1.00 d__Bacteria       p__Bacillota_A    c__Clostridia     o__Lachnospirales
10   EHA03305_bin.7  1.00 d__Bacteria      p__Bacteroidota   c__Bacteroidia      o__Bacteroidales
11  EHA03284_bin.37  1.00 d__Bacteria      p__Bacteroidota   c__Bacteroidia      o__Bacteroidales
12  EHA03294_bin.41  1.00 d__Bacteria      p__Bacteroidota   c__Bacteroidia      o__Bacteroidales
13  EHA03288_bin.14  1.00 d__Bacteria      p__Bacteroidota   c__Bacteroidia      o__Bacteroidales
14  EHA03306_bin.40  1.00 d__Bacteria      p__Bacteroidota   c__Bacteroidia      o__Bacteroidales
15  EHA03351_bin.61  1.00 d__Bacteria      p__Bacteroidota   c__Bacteroidia      o__Bacteroidales
16  EHA03291_bin.19  1.00 d__Bacteria      p__Bacteroidota   c__Bacteroidia      o__Bacteroidales
17  EHA04572_bin.27  1.00 d__Bacteria      p__Bacteroidota   c__Bacteroidia      o__Bacteroidales
18 EHA04588_bin.155  1.00 d__Bacteria      p__Bacteroidota   c__Bacteroidia      o__Bacteroidales
19  EHA03286_bin.19  1.00 d__Bacteria       p__Bacillota_A    c__Clostridia     o__Lachnospirales
20   EHA03343_bin.6  1.00 d__Bacteria      p__Bacteroidota   c__Bacteroidia      o__Bacteroidales
21  EHA03335_bin.54  1.00 d__Bacteria      p__Bacteroidota   c__Bacteroidia      o__Bacteroidales
22   EHA03288_bin.1  1.00 d__Bacteria       p__Bacillota_A    c__Clostridia     o__Lachnospirales
23  EHA03303_bin.18  1.00 d__Bacteria      p__Bacteroidota   c__Bacteroidia      o__Bacteroidales
24  EHA03331_bin.14  1.00 d__Bacteria      p__Bacteroidota   c__Bacteroidia      o__Bacteroidales
25   EHA04571_bin.1  1.00 d__Bacteria      p__Bacteroidota   c__Bacteroidia      o__Bacteroidales
26   EHA03282_bin.3  1.00 d__Bacteria       p__Bacillota_A    c__Clostridia o__Christensenellales
27  EHA03303_bin.19  1.00 d__Bacteria      p__Bacteroidota   c__Bacteroidia      o__Bacteroidales
28  EHA03292_bin.33  1.00 d__Bacteria      p__Bacteroidota   c__Bacteroidia      o__Bacteroidales
29   EHA03289_bin.1  1.00 d__Bacteria       p__Bacillota_A    c__Clostridia o__Christensenellales
30 EHA03305_bin.139  1.00 d__Bacteria       p__Bacillota_A    c__Clostridia     o__Lachnospirales
31  EHA03284_bin.21  1.00 d__Bacteria       p__Bacillota_A    c__Clostridia     o__Lachnospirales
32   EHA03335_bin.2  1.00 d__Bacteria      p__Bacteroidota   c__Bacteroidia      o__Bacteroidales
33  EHA03299_bin.29  1.00 d__Bacteria       p__Bacillota_A    c__Clostridia     o__Lachnospirales
34  EHA04587_bin.13  1.00 d__Bacteria      p__Bacteroidota   c__Bacteroidia      o__Bacteroidales
35  EHA04572_bin.12  1.00 d__Bacteria       p__Bacillota_A    c__Clostridia     o__Lachnospirales
36  EHA03281_bin.27  1.00 d__Bacteria      p__Bacteroidota   c__Bacteroidia      o__Bacteroidales
37 EHA04588_bin.163  1.00 d__Bacteria      p__Bacteroidota   c__Bacteroidia      o__Bacteroidales
38 EHA04588_bin.109  1.00 d__Bacteria      p__Bacteroidota   c__Bacteroidia      o__Bacteroidales
39  EHA03335_bin.59  1.00 d__Bacteria      p__Bacteroidota   c__Bacteroidia      o__Bacteroidales
40  EHA03331_bin.42  1.00 d__Bacteria      p__Bacteroidota   c__Bacteroidia      o__Bacteroidales
41  EHA03302_bin.23  1.00 d__Bacteria      p__Bacteroidota   c__Bacteroidia      o__Bacteroidales
42  EHA03294_bin.11  1.00 d__Bacteria       p__Bacillota_A    c__Clostridia     o__Lachnospirales
43  EHA04582_bin.20  1.00 d__Bacteria      p__Bacteroidota   c__Bacteroidia      o__Bacteroidales
44 EHA04588_bin.129  1.00 d__Bacteria      p__Bacteroidota   c__Bacteroidia      o__Bacteroidales
45  EHA03305_bin.54  1.00 d__Bacteria      p__Bacteroidota   c__Bacteroidia      o__Bacteroidales
46 EHA03305_bin.187  1.00 d__Bacteria       p__Bacillota_A    c__Clostridia     o__Lachnospirales
47  EHA04570_bin.11  0.75 d__Bacteria       p__Bacillota_A    c__Clostridia     o__Lachnospirales
48  EHA03329_bin.12  0.75 d__Bacteria      p__Bacteroidota   c__Bacteroidia      o__Bacteroidales
49   EHA03290_bin.8  0.75 d__Bacteria       p__Bacillota_A    c__Clostridia     o__Lachnospirales
50  EHA03282_bin.24  0.75 d__Bacteria      p__Bacteroidota   c__Bacteroidia      o__Bacteroidales
51  EHA03347_bin.46  0.75 d__Bacteria       p__Bacillota_A    c__Clostridia o__Christensenellales
52  EHA03305_bin.10  0.75 d__Bacteria      p__Bacteroidota   c__Bacteroidia      o__Bacteroidales
53  EHA04584_bin.27  0.75 d__Bacteria      p__Bacteroidota   c__Bacteroidia      o__Bacteroidales
54   EHA03288_bin.6  0.75 d__Bacteria       p__Bacillota_A    c__Clostridia     o__Lachnospirales
55  EHA04588_bin.27  0.75 d__Bacteria       p__Bacillota_A    c__Clostridia    o__Oscillospirales
56 EHA03305_bin.165  0.75 d__Bacteria p__Verrucomicrobiota c__Lentisphaeria      o__Victivallales
57   EHA03299_bin.8  0.75 d__Bacteria      p__Bacteroidota   c__Bacteroidia      o__Bacteroidales
58  EHA03292_bin.24  0.75 d__Bacteria       p__Bacillota_A    c__Clostridia     o__Lachnospirales
59   EHA03335_bin.4  0.75 d__Bacteria      p__Bacteroidota   c__Bacteroidia      o__Bacteroidales
60  EHA03347_bin.49  0.75 d__Bacteria       p__Bacillota_A    c__Clostridia o__Christensenellales
61  EHA03335_bin.23  0.75 d__Bacteria       p__Bacillota_A    c__Clostridia           o__UMGS1883
62  EHA03287_bin.10  0.75 d__Bacteria       p__Bacillota_A    c__Clostridia           o__UMGS1883
63  EHA03306_bin.65  0.75 d__Bacteria       p__Bacillota_A    c__Clostridia    o__Oscillospirales
64   EHA04587_bin.4  0.75 d__Bacteria       p__Bacillota_A    c__Clostridia    o__Oscillospirales
65   EHA04588_bin.9  0.75 d__Bacteria       p__Bacillota_A    c__Clostridia     o__Lachnospirales
66  EHA03304_bin.14  0.75 d__Bacteria       p__Bacillota_A    c__Clostridia           o__UMGS1883
67  EHA04569_bin.16  0.75 d__Bacteria       p__Bacillota_A    c__Clostridia    o__Oscillospirales
68  EHA03341_bin.13  0.75 d__Bacteria       p__Bacillota_A    c__Clostridia    o__Oscillospirales
69  EHA03306_bin.99  0.75 d__Bacteria       p__Bacillota_A    c__Clostridia     o__Lachnospirales
70  EHA04583_bin.16  0.75 d__Bacteria       p__Bacillota_A    c__Clostridia     o__Lachnospirales
71  EHA03300_bin.21  0.75 d__Bacteria       p__Bacillota_A    c__Clostridia     o__Lachnospirales
72  EHA03347_bin.26  0.75 d__Bacteria       p__Bacillota_A    c__Clostridia    o__Oscillospirales
73  EHA03288_bin.21  0.75 d__Bacteria       p__Bacillota_A    c__Clostridia     o__Lachnospirales
74  EHA03305_bin.48  0.75 d__Bacteria       p__Bacillota_A    c__Clostridia o__Christensenellales
75  EHA03347_bin.78  0.75 d__Bacteria       p__Bacillota_A    c__Clostridia    o__Oscillospirales
76 EHA03306_bin.194  0.75 d__Bacteria      p__Bacteroidota   c__Bacteroidia   o__Flavobacteriales
77  EHA03294_bin.21  0.75 d__Bacteria       p__Bacillota_A    c__Clostridia o__Christensenellales
78  EHA04570_bin.15  0.75 d__Bacteria       p__Bacillota_A    c__Clostridia     o__Lachnospirales
79  EHA04587_bin.16  0.75 d__Bacteria       p__Bacillota_A    c__Clostridia o__Christensenellales
80  EHA03290_bin.41  0.75 d__Bacteria       p__Bacillota_A    c__Clostridia     o__Lachnospirales
81  EHA03306_bin.93  0.75 d__Bacteria       p__Bacillota_A    c__Clostridia    o__Oscillospirales
82  EHA03335_bin.29  0.75 d__Bacteria       p__Bacillota_A    c__Clostridia    o__Oscillospirales
83  EHA04588_bin.75  0.75 d__Bacteria       p__Bacillota_A    c__Clostridia     o__Lachnospirales
                 family              genus                         species completeness contamination  length
1   f__Oscillospiraceae          g__RUG626                             s__        98.68          0.09 2717563
2     f__Bacteroidaceae     g__Bacteroides           s__Bacteroides caccae        93.33          0.92 4211779
3     f__Bacteroidaceae     g__Bacteroides                             s__        85.48          0.30 3379113
4     f__Bacteroidaceae   g__Phocaeicola_A    s__Phocaeicola_A sp900765575        98.44          0.99 4116127
5             f__CAG-74      g__Ventricola                             s__        95.10          1.64 2254008
6    f__Lachnospiraceae     g__Choladousia                             s__        97.25          1.25 4671245
7             f__CAG-74        g__UBA11524                             s__        97.95          0.43 3239667
8  f__Staphylococcaceae  g__Staphylococcus       s__Staphylococcus equorum        98.15          0.93 2867894
9    f__Lachnospiraceae  g__Eisenbergiella                             s__        86.47          0.42 2839523
10     f__Rikenellaceae     g__Alistipes_A   s__Alistipes_A pullistercoris        80.85          1.07 2007002
11    f__Bacteroidaceae     g__Bacteroides    s__Bacteroides xylanisolvens        50.02          1.84 3074582
12     f__Rikenellaceae       g__Alistipes        s__Alistipes onderdonkii        85.22          0.56 3111954
13    f__Tannerellaceae g__Parabacteroides   s__Parabacteroides distasonis        99.92          1.04 4517903
14    f__Tannerellaceae g__Parabacteroides       s__Parabacteroides merdae        95.00          1.15 3536678
15    f__Bacteroidaceae     g__Bacteroides    s__Bacteroides xylanisolvens        54.54          0.36 3343098
16    f__Bacteroidaceae     g__Phocaeicola         s__Phocaeicola vulgatus        75.41          7.84 3604540
17    f__Bacteroidaceae     g__Phocaeicola         s__Phocaeicola vulgatus        91.00          1.41 4625753
18    f__Bacteroidaceae   g__Phocaeicola_A                             s__        84.99          0.58 2866150
19   f__Lachnospiraceae  g__Eisenbergiella                             s__        92.06          0.05 2581303
20    f__Tannerellaceae g__Parabacteroides                             s__        52.37          9.76 5007474
21    f__Bacteroidaceae     g__Bacteroides     s__Bacteroides intestinalis        84.40          0.96 4955849
22   f__Lachnospiraceae  g__Eisenbergiella                             s__        91.13          3.59 4717828
23    f__Bacteroidaceae     g__Phocaeicola            s__Phocaeicola dorei       100.00          0.02 5099128
24    f__Bacteroidaceae     g__Bacteroides s__Bacteroides cellulosilyticus        71.05          0.68 4704445
25    f__Bacteroidaceae     g__Bacteroides        s__Bacteroides eggerthii        99.89          1.16 4889799
26            f__CAG-74      g__Ventricola                             s__        89.78          0.07 2436197
27    f__Bacteroidaceae     g__Bacteroides s__Bacteroides thetaiotaomicron        99.65          0.58 5784890
28     f__Rikenellaceae       g__Alistipes       s__Alistipes senegalensis        87.06          2.36 3508537
29            f__CAG-74      g__Ventricola                             s__        81.23          0.26 2045707
30   f__Lachnospiraceae        g__CAJMNU01                             s__        89.86          0.91 3464102
31   f__Lachnospiraceae  g__Eisenbergiella                             s__        98.68          0.00 2980924
32    f__Tannerellaceae g__Parabacteroides   s__Parabacteroides distasonis        83.11          0.46 3502905
33   f__Lachnospiraceae  g__Eisenbergiella                             s__        97.51          0.05 2710143
34    f__Bacteroidaceae     g__Phocaeicola         s__Phocaeicola sartorii        99.88          0.79 5360617
35   f__Lachnospiraceae  g__Eisenbergiella                             s__        94.67          0.67 3209166
36    f__Bacteroidaceae     g__Bacteroides s__Bacteroides cellulosilyticus        83.85          1.02 5526176
37    f__Bacteroidaceae     g__Phocaeicola         s__Phocaeicola vulgatus        76.67          4.85 3873955
38    f__Bacteroidaceae     g__Phocaeicola                             s__        83.28          0.04 2269172
39    f__Bacteroidaceae     g__Bacteroides    s__Bacteroides xylanisolvens        89.55          1.95 5681643
40    f__Bacteroidaceae     g__Bacteroides    s__Bacteroides xylanisolvens        87.77          1.56 4514808
41     f__Rikenellaceae       g__Alistipes       s__Alistipes senegalensis        91.07          1.61 3611824
42   f__Lachnospiraceae  g__Eisenbergiella                             s__        97.55          1.10 2772085
43    f__Bacteroidaceae     g__Bacteroides     s__Bacteroides intestinalis        98.74          3.02 5262979
44    f__Bacteroidaceae    g__Mediterranea                             s__        84.60          0.27 2458429
45    f__Bacteroidaceae     g__Bacteroides           s__Bacteroides nordii        86.46          2.91 4775769
46   f__Lachnospiraceae   g__Acetatifactor                             s__        83.86          5.94 2081955
47   f__Lachnospiraceae        g__UBA11774                             s__        98.12          0.39 2485558
48    f__Tannerellaceae g__Parabacteroides       s__Parabacteroides merdae        78.72          0.98 2799466
49   f__Lachnospiraceae            g__COE1                             s__       100.00          0.20 3572382
50    f__Bacteroidaceae     g__Phocaeicola            s__Phocaeicola dorei        67.52          2.70 3232002
51    f__Borkfalkiaceae      g__Gallimonas                             s__        91.16          0.09 1738834
52    f__Bacteroidaceae     g__Bacteroides s__Bacteroides cellulosilyticus        78.74          0.70 4821793
53    f__Bacteroidaceae     g__Bacteroides                             s__        51.88          6.75 3947610
54   f__Lachnospiraceae        g__HGM12545                             s__        76.13          3.48 2267120
55  f__Oscillospiraceae          g__UBA738                             s__        91.88          2.29 2503255
56    f__Victivallaceae     g__Victivallis                             s__        89.01          3.30 1970449
57    f__Bacteroidaceae     g__Bacteroides        s__Bacteroides uniformis        83.24          5.18 3484560
58   f__Lachnospiraceae         g__UBA3402                             s__        85.93          0.60 2588937
59     f__Rikenellaceae     g__Alistipes_A                             s__        76.39          1.16 1912399
60    f__Borkfalkiaceae      g__Gallimonas                             s__        77.78          2.06 1482397
61          f__UMGS1883        g__JAJQCX01                             s__        96.29          0.03 2311623
62          f__UMGS1883        g__JAJQCX01                             s__        93.35          0.43 2228574
63           f__CAG-272        g__CAKSQF01                             s__        72.26          1.30 1885396
64  f__Oscillospiraceae     g__Enterenecus                             s__        99.25          1.00 5115488
65   f__Lachnospiraceae         g__UBA3402                             s__        93.69          1.61 2069593
66          f__UMGS1883        g__JAJQCX01                             s__        93.11          0.60 2259580
67  f__Oscillospiraceae        g__CAJOIG01                             s__        84.02          1.35 2301527
68   f__Ruminococcaceae        g__Gemmiger                             s__        99.94          1.60 2427709
69   f__Lachnospiraceae   g__Acetatifactor                             s__        61.29          3.11 2080558
70   f__Lachnospiraceae     g__Choladousia                             s__        86.84          2.01 3189852
71   f__Lachnospiraceae  g__Eisenbergiella                             s__        96.57          0.30 2451036
72  f__Oscillospiraceae          g__RUG626                             s__       100.00          0.90 2823227
73   f__Lachnospiraceae  g__Eisenbergiella         s__Eisenbergiella porci        70.86          2.03 3844038
74            f__CAG-74      g__Ventricola                             s__        72.98          2.77 1939234
75  f__Oscillospiraceae        g__CAJOIG01                             s__        65.91          3.18 1927346
76           f__UBA1820     g__Merdimorpha      s__Merdimorpha sp003150615        99.49          0.02 2080137
77            f__CAG-74      g__Ventricola                             s__        73.33          3.89 1688509
78   f__Lachnospiraceae       g__Blautia_A                             s__        98.07          0.40 3924384
79            f__CAG-74                g__                             s__        82.41          5.34 2314477
80   f__Lachnospiraceae         g__UBA3402                             s__        89.35          0.80 3103732
81          f__JAAYOS01        g__CALXFK01                             s__        95.12          0.45 2515794
82          f__JAAYOS01        g__CALXFK01                             s__        94.70          0.87 1968744
83   f__Lachnospiraceae         g__UBA3402                             s__        89.05          3.42 2007340
 [ reached 'max' / getOption("max.print") -- omitted 682 rows ]

10.1 MCI

GIFTs_functions_community %>%
  rowMeans() %>%
  as_tibble(., rownames = "sample") %>%
  left_join(sample_metadata, by = join_by(sample == sample)) %>%
#  filter(time_point=="0_Wild") %>%
  group_by(diet) %>%
  summarise(MCI = mean(value), sd = sd(value))
# A tibble: 3 × 3
  diet         MCI     sd
  <chr>      <dbl>  <dbl>
1 Post_grass 0.240 0.0130
2 Pre_grass  0.249 0.0152
3 Wild       0.254 0.0206
MCI <- GIFTs_functions_community %>%
  rowMeans() %>%
  as_tibble(., rownames = "sample") %>%
  left_join(sample_metadata, by = join_by(sample == sample)) 
# %>% 
#   filter(diet!="Post_grass")

shapiro.test(MCI$value)

    Shapiro-Wilk normality test

data:  MCI$value
W = 0.98397, p-value = 0.8693
res.aov <- aov(value ~ diet, data=MCI)
summary(res.aov)
            Df   Sum Sq   Mean Sq F value Pr(>F)
diet         2 0.001317 0.0006583    2.39  0.107
Residuals   33 0.009090 0.0002755               

10.2 Community level plots

10.3 ANCOM-BC2

10.3.1 Captive vs Wild

10.3.1.1 Element level

10.4 Wilcoxon comparison

10.4.1 Community elements differences:

difference_table %>% 
  filter(group_color=="Wild")
   Elements    Pre_grass         Wild                                      Function          Element    Difference
1     D0702 2.176967e-01 4.215706e-01                   Alcohol degradation_Ethanol          Ethanol -0.2038739000
2     D0708 6.562387e-02 1.137517e-01                    Alcohol degradation_Phytol           Phytol -0.0481278300
3     D0705 2.174659e-01 2.932360e-01          Alcohol degradation_Propylene glycol Propylene glycol -0.0757701000
4     D0509 3.498560e-01 4.690221e-01               Amino acid degradation_Arginine         Arginine -0.1191661000
5     D0505 2.884142e-01 3.728710e-01                 Amino acid degradation_Valine           Valine -0.0844568000
6     B0307 2.568247e-01 3.888024e-01 Amino acid derivative biosynthesis_Spermidine       Spermidine -0.1319777000
7     D0903 1.047526e-03 2.363183e-03          Antibiotic degradation_Cephalosporin    Cephalosporin -0.0013156570
8     D0904 3.904555e-05 1.422616e-03              Antibiotic degradation_Oxacillin        Oxacillin -0.0013835705
9     B0902 9.761388e-06 3.556539e-04          Metallophore biosynthesis_Aerobactin       Aerobactin -0.0003458925
10    D0608 3.360954e-04 1.404321e-02         Nitrogen compound degradation_Betaine          Betaine -0.0137071121
11    D0306 2.292213e-01 3.300262e-01                    Sugar degradation_D-Xylose         D-Xylose -0.1008049000
12    D0806 2.616052e-05 9.531525e-04           Xenobiotic degradation_Anthranilate     Anthranilate -0.0009269920
13    D0811 3.527381e-06 1.281851e-04            Xenobiotic degradation_Benzoyl-CoA      Benzoyl-CoA -0.0001246577
14    D0808 1.952277e-06 7.113078e-05                 Xenobiotic degradation_Cumate           Cumate -0.0000691785
15    D0819 4.314553e-05 1.892106e-03                Xenobiotic degradation_Mercury          Mercury -0.0018489605
   group_color
1         Wild
2         Wild
3         Wild
4         Wild
5         Wild
6         Wild
7         Wild
8         Wild
9         Wild
10        Wild
11        Wild
12        Wild
13        Wild
14        Wild
15        Wild

10.4.1.1 Functional level

10.4.2 Before and after grass

10.4.2.1 Element level

10.4.2.2 Functional level

  taxon lfc_dietPre_grass p_dietPre_grass    Domain Function
1   S03        -0.1948368      0.01689626 Structure    Spore